Dear Amber community,
I want to generate a topology and coordinate file for an RNA structure with
parmCHI_YIL.bsc (from Ambertools 1.5, applied bugfix) for GB simulation.
Here is the input file for tleap
source leaprc.parmCHI_YIL.bsc
set default PBradii mbondi2
x = loadpdb RNA_ss_UUCG.pdb
saveamberparm x RNA_ss_UUCG_1_parmCHI_YIL.bsc.top RNA_ss_UUCG_1_B_form.crd
savepdb x RNA_ss_UUCG_1_B_form.pdb
quit
When I got the top file, there are some C atoms having radii of 2.2 A
instead of 1.7 A as I used ff10 force field. I used an in-house analysis
program to print this information.
C8 RG5 2.200
C6 RC 2.200
C6 RC 2.200
C8 RG 2.200
C8 RG 2.200
C6 RC3 2.200
Can you please tell me what happen? Is this because of the bug or I miss
something?
Best
NHAI
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Received on Thu Feb 16 2012 - 21:00:01 PST
